I just tested this in my dev environment, and I'm not able to replicate it. My classpath seems to be set properly.
Did you perhaps delete a runtime during a workspace session and then create a new one with the same name?
One workaround to force the classpath to reset for the dynamic web project would be to right-click the project, properties, then go to the "Targeted Runtimes" page, and uncheck your runtime. Press apply, then re-check it, and press apply. This will try to reset the classpath containers at least.
Where exactly are you seeing this build path error? You say you fiddled a bit and got it to reveal the error. Where was it? :)
Let's hope this is just a fluke of some type. Is it repeatable if done from a clean workspace? Any more information is definitely useful.